Mailman 3 May 2018 - Matplotlib-users

Creating a smooth surface in 3D
by Bala subramanian June 3, 2018

June 3, 2018

Dear mpl friends, My objective is to create a molecular surface using matplotlib. I used the snippet pasted below to create a series of spheres (attached png), drawn using the atom attributes (their positions and radius). From here, I would like to create a smooth surface which can depict the shape of the molecule surface (curves,cavities etc). Based on examples in net, I get a mixed feeling that either triangulation or making 3D grids are some directions to proceed. If anyone has some suggestions or better protocols for such task with some example data, it would be of great help to me. fig = plt.figure(figsize=(6,6),dpi=140) ax1 = fig.add_subplot(111, projection='3d') # Define spherical coordinates u, v = np.mgrid[0:2*np.pi:20j, 0:np.pi:10j] S = np.cos(u)*np.sin(v) C = np.sin(u)*np.sin(v) T = np.cos(v) for P,R in zip(positions,radii): ax1.plot_wireframe(R*S+P[0],R*C+P[1],R*T+P[2],color='r',alpha=0.4) Thanks in advance, Bala -- C. Balasubramanian

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How to create an animation of complicated figures without writing each image to file
by David Ketcheson May 31, 2018

May 31, 2018

I would like to create an animation from a very complicated plot. The plot is created by a lot of functions and it's not feasible for me to pass back the handles to all the objects that get added to the plot from all of those functions. One approach that works is to write each plot to a file and then create an animation by loading the images. Unfortunately, this doesn't look good, presumably because the images are first rasterized and then the resolution is altered. So I'd like to create an animation directly from a set of figures, when all I have are the figures. I've tried to use get_children() recursively to get all the artists and then use animation.ArtistAnimation(), but so far this only leads to an empty (blank) animation. Is it possible to do what I'm attempting? -David ________________________________ This message and its contents including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Re: [Matplotlib-users] How to create an animation of complicated figures without writing each image to file
by Thomas Caswell May 31, 2018

May 31, 2018

I do not know of a vector-based movie format, I think you have to rasterize at _some_ point. Try increasing the dpi or adjusting the encoding parameters / of ffmpeg (the defaults are not great for plots iirc). `to_jshtml` writes out movie file and then wraps it in minimal js player. Tom On Thu, May 31, 2018 at 9:14 AM David Ketcheson <dketch(a)gmail.com> wrote: > Thanks for your help! My replies are interspersed below. > > On Thu, May 31, 2018 at 3:38 PM, Thomas Caswell <tcaswell(a)gmail.com> > wrote: > >> If you have no control over the plotting functions, can not update the >> artists in place, or just have a sequence of Figure objects, the best >> approach is probably to so save each frame to png and then use an external >> program to (eg ffmpeg) stitch them together. Make sure that you are not >> using `bbox_inches='tight'`, tight_layour, or contrained layout (so every >> saved figure is the same size and the axes are in the same place). >> > > That's what I've been doing, but as I mentioned in my first message, the > output isn't what I want -- there are visible artifacts in the resulting > movie. Is there a way to do this without going to a rasterized graphics > format? > >> >> If you can re-use the same `Figure` object you can directly use the >> Writer classes is `matplotlib.animation`, see >> https://matplotlib.org/api/animation_api.html?highlight=animation#writer-cl… . >> Those instances are bound to a particular Figure, you _may_ be able to just >> re-set the figure (but not sure what other state we hold based on the >> initial figure that might need to be updated as well), at a minimum they >> should be a good starting point to write your self a "concatenate a list of >> figures into a movie" writer. >> > > I don't want to write a movie file; my goal is to end up with a > JSAnimation-style output (i.e., what you get from anim.to_jshtml()). I > don't see a writer class for that. > > >> >> On Thu, May 31, 2018 at 4:57 AM David Ketcheson < >> david.ketcheson(a)kaust.edu.sa> wrote: >> >>> I would like to create an animation from a very complicated plot. The >>> plot is created by a lot of functions and it's not feasible for me to pass >>> back the handles to all the objects that get added to the plot from all of >>> those functions. One approach that works is to write each plot to a file >>> and then create an animation by loading the images. Unfortunately, this >>> doesn't look good, presumably because the images are first rasterized and >>> then the resolution is altered. >>> >>> So I'd like to create an animation directly from a set of figures, when >>> all I have are the figures. I've tried to use get_children() recursively >>> to get all the artists and then use animation.ArtistAnimation(), but so >>> far this only leads to an empty (blank) animation. Is it possible to do >>> what I'm attempting? >>> >>> -David >>> >>> ------------------------------ >>> This message and its contents including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> _______________________________________________ >>> Matplotlib-users mailing list >>> Matplotlib-users(a)python.org >>> https://mail.python.org/mailman/listinfo/matplotlib-users >>> >>

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Help needed to fill_between two curves
by Akhilesh Nautiyal May 31, 2018

May 31, 2018

Dear Sir/Madam, I am plotting with matplotlib using two data files with different x and y ranges. I need to fill up the region between the two curves. I request you to kindly help me in this regard. I am attaching the files with this e-mail. the plot range should be between x->0.93 to 1.0 and y->0 to 0.25. Thanking you, Sincerely, akhliesh -- *********************************************************************************************** * Dr. Akhilesh Nautiyal * Assistant Professor * Department of Physics * Malaviya National Institute of Technology Jaipur * JLN Marg Jaipur-302017 * Mo: +91-9 <%2B91-9445520847>549657939 ***********************************************************************************************

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annotation arrow shrink
by Ilya Flyamer May 30, 2018

May 30, 2018

Hi all, I am trying to figure out how shrinkA works for arrows in annotations, and it seems very confusing from experimenting with it - is there an explanation somewhere online? I simply wanted to ensure that the arrow starts at the edge of the bounding box, but it's not so easy, it seems... Is this not the right way to do this, maybe? Thanks! Cheers, Ilya

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setting ticks on y axis
by dark0s May 22, 2018

May 22, 2018

Hi all, I create boxplots with Mathplotlib but the label in the y axis are: 0, 20, 40, 60, 80, 100. How can I set labels on the y axis to be 0, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100 and fit data according to them? Regards.

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Legends in single colour
by Kesavan Subburam May 17, 2018

May 17, 2018

Hi everyone, I'm writing on behalf of a friend who would like to plot his scatter plot markers in different colours and shapes, but the legends should only indicate shape but no colours, essentially single colour legends. Any ideas?

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facecolor for legend with alpha and shadow
by Slavin, Jonathan May 15, 2018

May 15, 2018

Hi all, I'm wondering why using shadow=True causes shading of the legend box when framealpha is set to a number. That is, if I do: fig,ax = plt.subplots() ax.plot(x,y1,label='y1') ax.plot(x,y2,label='y2') ax.legend(framealpha=0.5,shadow=True) The face color of the legend is gray. There doesn't seem to be any reason for this, so I'm assuming it's a bug. I've been looking through the docs and haven't found anything relevant - and haven't found any way around it other than turning off the shadow. Any help would be appreciated. Regards, Jon -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

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Script two planes
by alberto May 11, 2018

May 11, 2018

Hi I have a set of cartesian coordinates that define two plane of different atoms. Is it possible calculate distance and orthogonal projection? regards Alberto This is my data 24 test plane Pb -9.9300426676 4.1025666804 8.7420388123 Pb -4.0641923655 4.0198687706 1.6849745870 Pb -9.9866302880 4.1933336180 -1.3285956262 Pb -4.1207799859 4.1106357083 -8.3856598515 Pb -1.2684114297 4.1285931245 6.3124736259 Pb 4.5974388723 4.0458952147 -0.7445905994 Pb -1.3249990502 4.2193600622 -3.7581608126 Pb 4.5408512519 4.1366621524 -10.8152250379 Pb 7.3932198081 4.1546195686 3.8829084395 Pb 13.2590701101 4.0719216589 -3.1741557858 Pb 7.3366321877 4.2453865063 -6.1877259990 Pb 13.2024824897 4.1626885965 -13.2447902243 Mg -11.5004149207 -4.2961447648 13.2944782095 Mg -5.6345646187 -4.3788426745 6.2374139842 Mg -11.5570025411 -4.2053778271 3.2238437711 Mg -5.6911522391 -4.2880757369 -3.8332204543 Mg -2.8387836829 -4.2701183206 10.8649130231 Mg 3.0270666192 -4.3528162304 3.8078487978 Mg -2.8953713033 -4.1793513830 0.7942785847 Mg 2.9704789987 -4.2620492927 -6.2627856407 Mg 5.8228475550 -4.2440918765 8.4353478367 Mg 11.6886978570 -4.3267897862 1.3782836114 Mg 5.7662599345 -4.1533249388 -1.6352866017 Mg 11.6321102366 -4.2360228486 -8.6923508271

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bar plot with datetime x axis
by Steve Aplin May 10, 2018

May 10, 2018

Hello everyone, Having a bit of an adventure controlling the display of the x axis when plotting a pandas dataframe or series using pandas plot(), as in df.plot(kind='bar') or s.plot(kind='bar'). Here's the head of one column: 1996-01-01 180.0 1997-01-01 159.0 1998-01-01 159.0 1999-01-01 152.0 2000-01-01 121.0 Name: column A, dtype: float64 ... and here's its index: DatetimeIndex(['1996-01-01', '1997-01-01', '1998-01-01', '1999-01-01', '2000-01-01', ... ], dtype='datetime64[ns]', freq=None) I want to show a bunch of subplots, so my code looks like this: > from datetime import datetime > import matplotlib.pyplot as plt > import pandas as pd > import numpy as np > import matplotlib.dates as mdates > %matplotlib inline > > fig, axs = plt.subplots(9,2,figsize=(20,20),sharex=True) > for i,col in enumerate(df): > ax = df[col].plot(kind='bar',ax=axs[i,0]) > etc. ... which gives an x tick value for each index item (i.e. each bar), in full datetime format (YYYY-MM-DD 00:00:00), rotated 90 degrees. I don't want full datetime format, I just want the year portion. Googling the issue led me to trying this: fig.autofmt_xdate() > ... which rotates the labels, but still in full datetime format. So I tried adding > formatter = mdates.DateFormatter('%Y') > ax.xaxis.set_major_formatter(formatter) > which throws this error: ValueError: DateFormatter found a value of x=0, which is an illegal date. This usually occurs because you have not informed the axis that it is plotting dates, e.g., with ax.xaxis_date() ... which is a bit confusing, since the index is a pandas datetimeindex. Any ideas about how I could get my xaxis to not show just the year portion? Thanks in advance! Stephen E. Aplin Ottawa Canada

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